i have the same truck as you,and had the exact same problem with mine,so i took it to my dealer and first of all i needed my computer reflashed and updated with a cold start update,and secondly i had 2 injectors down also. i let the dealership fix it and sadly it cost me 1200 bucks parts and labor, but happily it runs like a brand new one now.

2005 6.0, no power!! No acceleration, cannot even get out of her own way. Had her in reverse, had to look to see if she was in neutral; as there was no movement what-so-ever. Visit to Dealer; all 8 fuel injectors, 8 glow plugs, and Y pipe changed. $4300 and dealer says there is nothing wrong with her. New EGR, air, oil and fuel filters. Running Royal Purple 15w40 syn. Only mods are volant cold air intake and after market exhaust. I am at a loss.

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